You can add Windows Defender to the exclusion list for RT checks. It seems that it scans itself whenever it runs.

(Windows 8.1) Go to Control Panel > Windows Defender, click on the 'Settings' tab, browse to C:\Program Files\Windows Defender and select MsMpEng.exe, Hit 'Add' and 'Save changes' and that should help quite a lot.

It should be noted that now your computer will be vulnerable to any exploit that uses that file, but that beats being vulnerable to any infected file should you turn it off or exclude your entire C:\ drive as somebody else suggests.